QIIME/en: Difference between revisions

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 #SBATCH --account=def-someuser
-singularity exec -B /home -B /project -B /scratch qiime2-2019.10.sif \
+singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \
-   qiime tools import \
+  -B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \
-  --type 'FeatureData[Sequence]' \
+   qiime tools import --type 'FeatureData[Sequence]' \
-   --input-path /path/to/some_fastafile.fa \
+   --input-path /inputs/some_fastafile.fa \
-   --output-path /path/to/some_output_feature.qza
+   --output-path /outputs/some_output_feature.qza
-singularity exec -B /home -B /project -B /scratch qiime2-2019.10.sif \
+singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \
+  -B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \
    qiime tools import \
    --type 'FeatureData[Taxonomy]' \
    --input-format HeaderlessTSVTaxonomyFormat \
-   --input-path /path/to/some_taxonomy_file.tax \
+   --input-path /inputs/some_taxonomy_file.tax \
-   --output-path /path/to/some_output_ref-taxonomy.qza
+   --output-path /outputs/some_output_ref-taxonomy.qza
-singularity exec -B /home -B /project -B /scratch qiime2-2019.10.sif \
+singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \
+  -B /projects/someuser/path/to/inputs:/inputs qiime2-2019.10.sif \
    qiime feature-classifier fit-classifier-naive-bayes \
-   --i-reference-reads  /path/to/some_output_feature.qza \
+   --i-reference-reads  /outputs/some_output_feature.qza \
-   --i-reference-taxonomy /path/to/some_output_ref-taxonomy.qza \
+   --i-reference-taxonomy /outputs/some_output_ref-taxonomy.qza \
-   --o-classifier /path/to/some_output_classifier.qza
+   --o-classifier /outputs/some_output_classifier.qza
 </pre>